NAME

Bio::Graphics::Glyph::dna - The "dna" glyph

SYNOPSIS

  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

This glyph draws DNA sequences. At high magnifications, this glyph will draw the actual base pairs of the sequence (both strands). At low magnifications, the glyph will plot the GC content. By default, the GC calculation will use non-overlapping bins, but this can be changed by specifying the gc_window option, in which case, a sliding window calculation will be used.

For this glyph to work, the feature must return a Bio::PrimarySeq DNA object in response to the seq() method. For example, you can use a Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq like this:

  my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
  my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end => 800 );
  $feature->attach_seq($dna);
  $panel->add_track( $feature, -glyph => 'dna' );

A Bio::Graphics::Feature object may also be used.

OPTIONS

The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation.

  Option      Description                      Default
  ------      -----------                      -------

  -fgcolor      Foreground color               black

  -outlinecolor Synonym for -fgcolor

  -bgcolor      Background color               turquoise

  -fillcolor    Synonym for -bgcolor

  -linewidth    Line width                     1

  -height       Height of glyph                10

  -font         Glyph font                     gdSmallFont

  -connector    Connector type                 0 (false)

  -connector_color
                Connector color                black

  -label        Whether to draw a label        0 (false)

  -description  Whether to draw a description  0 (false)

  -hilite       Highlight color                undef (no color)

In addition to the common options, the following glyph-specific options are recognized:

  Option      Description               Default
  ------      -----------               -------

  -do_gc      Whether to draw the GC      true
              graph at low mags

  -gc_window  Size of the sliding window  E<lt>noneE<gt>
              to use in the GC content 
              calculation.  If this is 
              not defined, non-
              overlapping bins will be 
              used. If this is set to
              "auto", then the glyph will
              choose a window equal to
              1% of the interval.

  -gc_bins    Fixed number of intervals   100
              to sample across the
              panel.

  -axis_color Color of the vertical axes  fgcolor
              in the GC content graph

  -strand      Show both forward and      auto
              reverse strand, one of
              "forward", "reverse",
              "both" or "auto".
              In "auto" mode,
              +1 strand features will
              show the plus strand
              -1 strand features will
              show the reverse complement
              and strandless features will
              show both

NOTE: -gc_window=>'auto' gives nice results and is recommended for drawing GC content. The GC content axes draw slightly outside the panel, so you may wish to add some extra padding on the right and left.

BUGS

Please report them.

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Sliding window GC calculation added by Peter Ashton <pda@sanger.ac.uk>.